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add create Dockerfile from sessionInfo object in sessionInfo.Rdata
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also some code restructuring and extraction of bespoke dependency installers
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@nuest
nuest committed Mar 23, 2018
1 parent 59b2f7a commit 34b1756
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Showing 24 changed files with 554 additions and 396 deletions.
1 change: 1 addition & 0 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,7 @@ Collate:
'containerit.R'
'defaults.R'
'dockerfile.R'
'package-installation-bespoke.R'
'package-installation-methods.R'
'sessionInfo-localbuild-methods.R'
'utility-functions.R'
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1 change: 1 addition & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ export(dockerfile)
export(getGitHubRef)
export(getImageForVersion)
export(getRVersionTag)
export(getSessionInfoFromRdata)
export(parseFrom)
exportClasses(Add)
exportClasses(Arg)
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2 changes: 1 addition & 1 deletion R/Class-Run.R
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ setClass("Run_shell",
# or ["param1","param2"] (for CMD as default parameters to ENTRYPOINT)

commands <- methods::slot(obj, "commands")
string <- paste(commands, collapse = " \\\n && ")
string <- paste(commands, collapse = " \\\n && ")
return(string)
}

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129 changes: 63 additions & 66 deletions R/dockerfile.R
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Original file line number Diff line number Diff line change
Expand Up @@ -28,14 +28,12 @@
#' This executes the whole file to obtain a complete \code{sessionInfo} object, see section "Based on \code{sessionInfo}", and copies required files and documents into the container.
#'
#' @param from The source of the information to construct the Dockerfile. Can be a \code{sessionInfo} object, a path to a file, or the path to a workspace). If \code{NULL} then no automatic derivation of dependencies happens.
#' @param image (\linkS4class{From}-object or character) Specifes the image that shall be used for the Docker container (\code{FROM} instruction).
#' By default, the image is determinded from the given session. Alternatively, use \code{getImageForVersion(..)} to get an existing image for a manually defined version of R, matching the version with tags from the base image rocker/r-ver (see details about the rocker/r-ver at \url{'https://hub.docker.com/r/rocker/r-ver/'}). Or provide a correct image name yourself.
#' @param maintainer Specify the maintainer of the dockerfile. See documentation at \url{'https://docs.docker.com/engine/reference/builder/#maintainer'}. Defaults to \code{Sys.info()[["user"]]}. Can be removed with \code{NULL}.
#' @param save_image When TRUE, it calls \link[base]{save.image} and include the resulting .RData in the container's working directory.
#' Alternatively, you can pass a list of objects to be saved, which may also include arguments to be passed down to \code{save}. E.g. save_image = list("object1", "object2", file = "path/in/wd/filename.RData").
#' \code{save} will be called with default arguments file = ".RData" and envir = .GlobalEnv
#' @param maintainer Specify the maintainer of the dockerfile. See documentation at \url{'https://docs.docker.com/engine/reference/builder/#maintainer'}. Defaults to \code{Sys.info()[["user"]]}. Can be removed with \code{NULL}.
#' @param r_version (character) optionally specify the R version that should run inside the container. By default, the R version from the given sessioninfo is used (if applicable) or the version of the currently running R instance
#' @param image (From-object or character) optionally specify the image that shall be used for the Docker container (FROM-statement)
#' By default, the image is determinded from the given r_version, while the version is matched with tags from the base image rocker/r-ver
#' see details about the rocker/r-ver at \url{'https://hub.docker.com/r/rocker/r-ver/'}
#' @param env optionally specify environment variables to be included in the image. See documentation: \url{'https://docs.docker.com/engine/reference/builder/#env}
#' @param soft (boolean) Whether to include soft dependencies when system dependencies are installed, default is no.
#' @param offline (boolean) Whether to use an online database to detect system dependencies or use local package information (slower!), default is no.
Expand All @@ -47,6 +45,7 @@
#' @param vanilla Whether to use an empty vanilla session when packaging scripts and markdown files (equivalent to \code{R --vanilla})
#' @param silent Whether or not to print information during execution
#' @param versioned_libs [EXPERIMENTAL] Whether it shall be attempted to match versions of linked external libraries
#' @param versioned_packages [EXPERIMENTAL] Whether it shall be attempted to match versions of R packages
#'
#' @return An object of class Dockerfile
#'
Expand All @@ -59,14 +58,13 @@
#' print(dockerfile)
#'
dockerfile <- function(from = utils::sessionInfo(),
save_image = FALSE,
image = getImageForVersion(getRVersionTag(from)),
maintainer = Sys.info()[["user"]],
r_version = getRVersionTag(from),
image = getImageForVersion(r_version),
save_image = FALSE,
env = list(generator = paste("containerit", utils::packageVersion("containerit"))),
soft = FALSE,
offline = FALSE,
copy = "script",
copy = NA, # "script",
# nolint start
container_workdir = "/payload/",
# nolint end
Expand All @@ -75,19 +73,20 @@ dockerfile <- function(from = utils::sessionInfo(),
add_self = FALSE,
vanilla = TRUE,
silent = FALSE,
versioned_libs = FALSE) {
versioned_libs = FALSE,
versioned_packages = FALSE) {
if (silent) {
invisible(futile.logger::flog.threshold(futile.logger::WARN))
}

futile.logger::flog.debug("Creating a new Dockerfile from '%s'", from)
.dockerfile <- NA
.originalFrom <- class(from)

#parse From-object from string if necessary
if (is.character(image)) {
image <- parseFrom(image)
}
futile.logger::flog.debug("Creating a new Dockerfile from '%s' with base image %s", from, toString(image))

if (is.character(maintainer)) {
.label <- Label_Maintainer(maintainer)
Expand Down Expand Up @@ -150,12 +149,13 @@ dockerfile <- function(from = utils::sessionInfo(),
futile.logger::flog.debug("Creating from sessionInfo object")
.dockerfile <-
dockerfileFromSession(
session = from,
.dockerfile = .dockerfile,
session = from,
soft = soft,
offline = offline,
add_self = add_self,
versioned_libs = versioned_libs,
versioned_packages = versioned_packages,
workdir = workdir
)
} else if (inherits(x = from, "character")) {
Expand All @@ -175,10 +175,11 @@ dockerfile <- function(from = utils::sessionInfo(),
vanilla = vanilla,
silent = silent,
versioned_libs = versioned_libs,
versioned_packages = versioned_packages,
workdir = workdir
)
} else if (file.exists(from)) {
futile.logger::flog.debug("'%s' is a file")
futile.logger::flog.debug("'%s' is a file", from)
.originalFrom <- from
.dockerfile <-
dockerfileFromFile(
Expand All @@ -191,29 +192,27 @@ dockerfile <- function(from = utils::sessionInfo(),
vanilla = vanilla,
silent = silent,
versioned_libs = versioned_libs,
versioned_packages = versioned_packages,
workdir = workdir
)
} else {
stop("Unsupported string for 'from' argument (not a file, not a directory): ", from)
}
} else if (is.expression(from) ||
(is.list(from) && all(sapply(from, is.expression)))) {
futile.logger::flog.debug("Creating from expession: %s", toString(from))

.sessionInfo <-
clean_session(expr = from,
slave = silent,
vanilla = vanilla)
.dockerfile <-
dockerfileFromSession(
session = .sessionInfo,
.dockerfile = .dockerfile,
soft = soft,
offline = offline,
add_self = add_self,
versioned_libs = versioned_libs,
workdir = workdir
)
futile.logger::flog.debug("Creating from expession: '%s' with a clean session", toString(from))

.sessionInfo <- clean_session(expr = from,
slave = silent,
vanilla = vanilla)
.dockerfile <- dockerfileFromSession(.dockerfile = .dockerfile,
session = .sessionInfo,
soft = soft,
offline = offline,
add_self = add_self,
versioned_libs = versioned_libs,
versioned_packages = versioned_packages,
workdir = workdir)
} else {
stop("Unsupported 'from': ", class(from), " ", from)
}
Expand Down Expand Up @@ -244,6 +243,7 @@ dockerfileFromSession <- function(session,
offline,
add_self,
versioned_libs,
versioned_packages,
workdir) {
futile.logger::flog.debug("Creating from sessionInfo")

Expand All @@ -259,20 +259,21 @@ dockerfileFromSession <- function(session,
image_name = .dockerfile@image@image
if (image_name %in% .debian_images) {
platform = .debian_platform
futile.logger::flog.debug("Found image %s in list of debian images.")
futile.logger::flog.debug("Found image %s in list of Debian images", image_name)
}
futile.logger::flog.debug("Detected platform %s", platform)
futile.logger::flog.debug("Detected platform: %s", platform)

.dockerfile <-
.create_run_install(
.dockerfile = .dockerfile,
pkgs = pkgs,
platform = platform,
soft = soft,
offline = offline,
versioned_libs = versioned_libs,
workdir = workdir # will be added as last instruction
)
.dockerfile <- .create_run_install(
dockerfile = .dockerfile,
pkgs = pkgs,
platform = platform,
soft = soft,
offline = offline,
versioned_libs = versioned_libs,
versioned_packages = versioned_packages)

# after all installation is done, set the workdir
addInstruction(.dockerfile) <- workdir

return(.dockerfile)
}
Expand All @@ -287,11 +288,11 @@ dockerfileFromFile <-
vanilla,
silent,
versioned_libs,
versioned_packages,
workdir) {
futile.logger::flog.debug("Creating from file")
#################################################

# prepare context ( = working directory) and normalize paths:
#################################################
context = normalizePath(getwd())
file = normalizePath(file)

Expand All @@ -304,9 +305,7 @@ dockerfileFromFile <-
# make sure that the path is relative to context
rel_path <- .makeRelative(file, context)

####################################################
# execute script / markdowns and obtain sessioninfo
#####################################################
# execute script / markdowns or read Rdata file to obtain sessioninfo
if (stringr::str_detect(file, ".R$")) {
futile.logger::flog.info("Executing R script file in %s locally.", rel_path)
sessionInfo <-
Expand All @@ -316,7 +315,7 @@ dockerfileFromFile <-
slave = silent,
echo = !silent
)
} else if (stringr::str_detect(file, ".Rmd$")) {
} else if (stringr::str_detect(file, ".Rmd$")) {
futile.logger::flog.info("Processing the given file %s locally using rmarkdown::render(...)", rel_path)
sessionInfo <-
obtain_localSessionInfo(
Expand All @@ -325,13 +324,13 @@ dockerfileFromFile <-
slave = silent,
echo = !silent
)
} else if (stringr::str_detect(file, ".Rdata$")) {
sessionInfo <- getSessionInfoFromRdata(file)
} else{
futile.logger::flog.info("The supplied file %s has no known extension. containerit will handle it as an R script for packaging.", rel_path)
}

####################################################
# append system dependencies and package installation instructions
####################################################
.dockerfile <-
dockerfileFromSession(
session = sessionInfo,
Expand All @@ -340,11 +339,11 @@ dockerfileFromFile <-
offline = offline,
add_self = add_self,
versioned_libs = versioned_libs,
versioned_packages = versioned_packages,
workdir = workdir
)

## working directory must be set before. Now add copy instructions
####################################################
if (!is.null(copy) && !is.na(copy)) {
copy = unlist(copy)
if (!is.character(copy)) {
Expand Down Expand Up @@ -400,6 +399,7 @@ dockerfileFromWorkspace <-
vanilla,
silent,
versioned_libs,
versioned_packages,
workdir) {
futile.logger::flog.debug("Creating from workspace directory")
target_file <- NULL #file to be packaged
Expand Down Expand Up @@ -453,13 +453,13 @@ dockerfileFromWorkspace <-
vanilla = vanilla,
silent = silent,
versioned_libs = versioned_libs,
versioned_packages = versioned_packages,
workdir = workdir
)
return(.df)
}



#' getImageForVersion-method
#'
#' Get a suitable Rocker image based on the R version.
Expand All @@ -483,7 +483,7 @@ getImageForVersion <- function(r_version, nearest = TRUE) {
image <- From(.rocker_images[["versioned"]], tag = r_version)

closestMatch <- function(version, versions) {
if(version %in% versions) return(version);
if (version %in% versions) return(version);

factors <- list(major = 1000000, minor = 1000, patch = 1)

Expand All @@ -506,23 +506,21 @@ getImageForVersion <- function(r_version, nearest = TRUE) {
}

if (!r_version %in% tags) {
if(nearest) {
if (nearest) {
# get numeric versions with all parts (maj.min.minor), i.e. two dots
numeric_tags <- tags[which(grepl("\\d.\\d.\\d", tags))]
closest <- as.character(closestMatch(r_version, numeric_tags))
image <- From(.rocker_images[["versioned"]], tag = closest)

warning(
"No Docker image found for the given R version, returning closest match: ",
closest,
" Existing tags (list only available when online): ",
paste(tags, collapse = " ")
warning("No Docker image found for the given R version, returning closest match: ",
closest,
" Existing tags (list only available when online): ",
paste(tags, collapse = " ")
)
} else {
warning(
"No Docker image found for the given R version, returning input. ",
"Existing tags (list only available when online): ",
paste(tags, collapse = " ")
warning("No Docker image found for the given R version, returning input. ",
"Existing tags (list only available when online): ",
paste(tags, collapse = " ")
)
}
}
Expand All @@ -531,10 +529,9 @@ getImageForVersion <- function(r_version, nearest = TRUE) {
}

.tagsfromRemoteImage <- function(image) {
urlstr <-
paste0("https://registry.hub.docker.com/v2/repositories/",
image,
"/tags/?page_size=9999")
urlstr <- paste0("https://registry.hub.docker.com/v2/repositories/",
image,
"/tags/?page_size=9999")

tryCatch({
con <- url(urlstr)
Expand Down
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